Generally speaking try/except will only catch python errors. To catch java errors in Ignition, you have to import them, for instance to catch an error that the database throws you would need
import java.lang.Exception
try:
system.db.runUpdateQuery("somequery")
except Exception, e:
## catches python errors
except java.lang.Exception, e:
## Catches database thrown errors
Looking at your stack trace it looks like ultimately you get java.util.concurrent.TimeoutException so that is the exception you would need to import and catch specifically. It doesn’t look like you get much info back (null) but at least catching this specifically you could start logging those instances and perhaps some sort of pattern that is causing it.